Thanks everyone for your responses. I wanted to answer this yesterday but I didn't have the time to do so.

Ok, the PMR number was 27035,000,613. It's closed now because I had to try to split the process, and since the problem doesn't occur every weekend, it could took a while to see another occurrence. The NSD file was sent on that occasion. I can open a new one after I collect the data Hamed said in his previous post.

I already have some debug parameters on the notes.ini, but not everyone listed there, so I'll set them and wait. 

Regarding Steve question, the first time this problem occurs, I restarted the server and it crashed again after a few minutes. Removing transaction logs (and creating new ones) was the solution. I confess I didn't try this last time, I simply remove them to save time since I don't mind the server running consistency checks on all databases. It happened on sunday, our databases are controlled in size so the check is relatively quick, and very very few users may check mails that day.